Fig. 4

Small RNA-directed methylation of transposons during embryogenesis. a, c Boxplots of 24-nt siRNA levels in wild-type and nrpd1a mutant floral buds (fb), early heart embryos (eh), and leaves (lf) derived from euchromatic (a) or heterochromatic (c) TEs. Thick horizontal bars indicate medians, and the top and bottom edges of the box indicate the 75th and 25th percentiles, respectively. b, d Boxplots of CHH methylation levels in wild-type and nrpd1a mutant floral buds (fb), early heart embryos (eh), bent cotyledon embryos (bc), and leaves (lf) for euchromatic (b) or long heterochromatic (d) TEs. P values < 0.0001 based on Mann-Whitney U test of methylation differences between wild-type and nrpd1a tissues are represented by * in d. All differences displayed in a–c had P values < 0.0001. e, f Boxplots of CHH methylation differences between nrpd1a and wild-type tissues for long heterochromatic TEs in either CWA (e) or non-CWA (f) contexts. g, h Metaplots of average weighted CHH methylation percentages of long heterochromatic TEs in nrpd1a and wild-type tissues in either CWA (g) or non-CWA (h) contexts. See also Additional file 2: Figure S4